That's interesting. I didn't know that any of the major manufacturers had cameras that would output to HD mkv files.
I convert blu ray HD footage to dvd-video quite often with AVStoDVD, so I know this will generally work for that type of conversion. It has no editing capability however. For editing you might want to try the Vegas software I linked earlier, since it is a Sony product and specifically has HD support.
Normally the cameras come with their own software. Did yours not?